I am not sure how to get hold of the command line. Here is the "Other Flags" entry of the Visual Studio project properties:
--ws:"Bundle" --project:"D:\fsharp\projects\Strts.messedup\Creator\Creator.fsproj" --wsoutput:"D:\fsharp\projects\Strts.messedup\Creator" --wsoutput:"Content" --jsmap

Hi, checking full command line in VS: Ctrl-Q "msbuild" then set project build output verbosity to Detailed.

The log will be long, but you can search for wsfsc.exe.

I am still not sure about what can cause this. Have you also tested with 4.2-beta? There are changes around command lines there, adding a new option to configure settings with a wsconfig.json. (A bugfix release is coming really soon, fixing debugging experience.)

Yes, I can see that there are multiple --ws:Bundle flags, and WebSharper 4.1 does not like this (although there is no strong reason, just to invalidate unexpected input).

My guess would be that there are multiple Import tags for WebSharp.FSharp.targets files in the project file, maybe old ones not cleaned up properly by a NuGet update. Can you make sure that there is only one? (Possibly by uninstalling WS packages, removing anything related from project file then reinstalling. Or convert to Paket and remove older NuGet references.)

It seems that indeed I did not properly deinstall the old version, so that I had two import lines in the project file.
But now, after deinstalling both versions and reinstalling 4.1.6, I have just a single import of the target file: